TSpred: a robust prediction framework for TCR-epitope interactions using paired chain TCR sequence data.

MOTIVATION: Prediction of T-cell receptor (TCR)-epitope interactions is important for many applications in biomedical research, such as cancer immunotherapy and vaccine design. The prediction of TCR-epitope interactions remains challenging especially for novel epitopes, due to the scarcity of available data. RESULTS: We propose TSpred, a new deep learning approach for the pan-specific prediction of TCR binding specificity based on paired chain TCR data. We develop a robust model that generalizes well to unseen epitopes by combining the predictive power of CNN and the attention mechanism. In particular, we design a reciprocal attention mechanism which focuses on extracting the patterns underlying TCR-epitope interactions. Upon a comprehensive evaluation of our model, we find that TSpred achieves state-of-the-art performances in both seen and unseen epitope specificity prediction tasks. Also, compared to other predictors, TSpred is more robust to bias related to peptide imbalance in the dataset. In addition, the reciprocal attention component of our model allows for model interpretability by capturing structurally important binding regions. Results indicate that TSpred is a robust and reliable method for the task of TCR-epitope binding prediction. AVAILABILITY AND IMPLEMENTATION: Source code is available at https://github.com/ha01994/TSpred.

Low-dose glucocorticoid increase the risk of fracture in postmenopausal women with low bone mass: a retrospective cohort study.

Long-term glucocorticoids (GCs) treatment is associated with osteoporosis and fractures. We investigated whether low-dose GC treatment also increased the risk of osteoporotic fractures, and the results showed that even low-dose GC treatment increased the risk of osteoporotic fractures, especially spine fractures. PURPOSE: The effect of low-dose glucocorticoid (GC) therapy on the fracture risk in postmenopausal women with low bone mass was investigated. METHODS: 119,790 66-year-old postmenopausal women with low bone mass based on bone mineral density (BMD) results were included. GC group consisted of patients who had been prescribed oral GCs within 6 months of BMD testing. In GC group, GCs dosage was calculated by a defined daily dose (DDD), and divided into five groups according to GC usage (Group 1[G1]; < 11.25 DDDs, G2; ≥ 11.25, < 22.5 DDDs, G3; ≥ 22.5, < 45 DDDs, G4; ≥ 45, < 90 DDDs, G5; ≥ 90 DDDs). The risk of major osteoporotic fractures (MOF) and non-MOF was analyzed and compared with that of the control group during the 1-year follow-up. RESULTS: The risk of total fracture was higher in G3-G5 than in the control group (G3, hazard ratio (HR) 1.25, 95% confidence interval [CI] 1.07-1.46; G4, 1.37 [1.13-1.66]; G5 1.45 [1.08-1.94]). The risk of MOF was higher in all groups except G2 than in the control group (G1, 1.23 [1.05-1.45]; G3, 1.37 [1.11-1.68]; G4, 1.41 [1.09-1.83]; G5, 1.66 [1.14-2.42]). The risk of spine fracture was significantly higher in all GC groups except G2 than in the control group. The risk of non-MOF was higher only in G4 than in the control group (G4, 1.48 [1.13-1.94]). CONCLUSION: Low-dose GC therapy can increase the risk of osteoporotic fractures, particularly spine fractures, in postmenopausal women with low bone mass.

Genetic and Phenotypic Diversity of Listeria monocytogenes in Pig Slaughterhouses in Korea.

Listeria monocytogenes is a foodborne pathogen that has variable subtypes associated with human listeriosis and occurs in food and processing environments. This study was conducted to provide the genetic and phenotypic characterization of L. monocytogenes in pig carcasses and environments of slaughterhouses in Korea. A total of 22 L. monocytogenes were isolated from eight of 26 pig slaughterhouses between 2020 and 2022, and the most common serotype was 1/2c (40.9%), followed by serotypes 1/2b (31.8%) and 1/2a (27.3%). The isolates showed a significantly high prevalence of virulence genes located in Listeria pathogenicity island-1 (LIPI-1) and internalins (90.9-100%; p < 0.05). However, the prevalence rates of llsX, ptsA, and stress survival islet-1 (SSI-1) located in LIPI-3, LIPI-4, and SSI were only 9.1%, 22.7%, and 31.8%, respectively. In addition, among the epidemic clones (EC), ECI, ECII, ECIII, and ECV, only one isolate was represented as ECV. Isolates identified from the same slaughterhouses were divided into two or more pulsotypes, except for two slaughterhouses. Furthermore, the seven STs were classified into seven clonal complexes (CCs) (CC8, CC9, CC37, CC87, CC121, CC155, and CC288), and all CCs belonged to lineages I (31.8%) and II (68.1%). Interestingly, the isolates showed a high prevalence of oxacillin resistance (59.1%), and most isolates of the serotypes 1/2a and 1/2b exhibited oxacillin resistance, whereas only one of nine serotype 1/2c isolates exhibited oxacillin resistance. These results provide the genetic diversity of L. monocytogenes in pig carcasses and environments of slaughterhouses, and continuous monitoring will be helpful in predicting food safety risks.

Nursing diagnoses as factors associated with delirium among intensive care unit patients with sepsis: A retrospective correlational study.

AIMS: To examine whether nursing diagnoses were associated with delirium in patients with sepsis. BACKGROUND: Nursing diagnosis is a nurse's clinical judgement about clients' current or potential health conditions. Delirium is regarded as an important nurse-sensitive outcome. Nonetheless, nursing diagnoses associated with delirium have not yet been identified. DESIGN: Retrospective correlational study. METHODS: This study was carried out from December 2021 to January 2023. We analysed electronic health records of patients with sepsis admitted to the intensive care units (ICUs) of a tertiary hospital in Seoul, South Korea. Delirium was defined based on the Intensive Care Delirium Screening Checklist score. Nursing diagnoses established within 24 h of admission to the ICU were included and were based on the North American Nursing Diagnosis Association diagnostic classification. The data were analysed using logistic regression. Demographics, comorbidities, procedures and physiological measures were adjusted. Regression model was evaluated via receiver operating characteristic curve, Nagelkerke R2, accuracy and F1 score. RESULTS: The prevalence of delirium in patients with sepsis was 51.8%. Ineffective breathing patterns, decreased cardiac output and impaired skin integrity were significant nursing diagnoses related to delirium. Age ≥ 65 years, Acute Physiology and Chronic Health Evaluation II score, mechanical ventilation, continuous renal replacement therapy, physical restraint and comatose state were also associated with delirium in patients with sepsis. The area under the receiver operating characteristic curve was 0.806. CONCLUSION: Ineffective breathing patterns, decreased cardiac output and impaired skin integrity could manifest as prodromal symptoms of delirium among patients with sepsis. IMPACT: The prodromal symptoms of delirium revealed through nursing diagnoses can be efficiently used to identify high-risk groups for delirium. The use of nursing diagnosis system should be recommended in clinical practice caring for sepsis patients. REPORTING METHODS: STROBE checklist. PATIENT OR PUBLIC CONTRIBUTION: No patient or public involvement.

Vitamin D Attenuates Fibrotic Properties of Fibrous Dysplasia-Derived Cells for the Transit towards Osteocytic Phenotype.

Fibrous dysplasia (FD) poses a therapeutic challenge due to the dysregulated extracellular matrix (ECM) accumulation within affected bone tissues. In this study, we investigate the therapeutic potential of 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) in managing FD by examining its effects on FD-derived cells in vitro. Our findings demonstrate that 1,25(OH)2D3 treatment attenuates the pro-fibrotic phenotype of FD-derived cells by suppressing the expression of key pro-fibrotic markers and inhibiting cell proliferation and migration. Moreover, 1,25(OH)2D3 enhances mineralization by attenuating pre-osteoblastic cellular hyperactivity and promoting maturation towards an osteocytic phenotype. These results offer valuable insights into potential treatments for FD, highlighting the role of 1,25(OH)2D3 in modulating the pathological properties of FD-derived cells.

Prevalence, genetic characteristics, and antimicrobial resistance of Clostridioides difficile isolates from horses in Korea.

OBJECTIVES: Clostridioides difficile is an etiological agent of enteric diseases in humans and animals. Animals are considered a potential reservoir due to the genetic and antimicrobial resistance similarities between human and animal C. difficile isolates. In this study, we evaluated the genetic characteristics and antimicrobial resistance profiles of C. difficile isolated from 942 fecal samples collected from horses in South Korea during 2019-2020. METHODS: The C. difficile isolates were tested for toxin genes including tcdA (A), tcdB (B), and cdtAB (CDT) and deletions of the tcdC gene by PCR. In addition, ribotyping, multilocus sequence typing, and antimicrobial susceptibility tests were performed. RESULTS: Twenty-three (2.4%) C. difficile isolates were associated with diarrhea in foals under 1 year old during the spring-summer period. Of these, 82.6% were toxigenic strains, determined to be A+B+CDT+ (52.1%) or A+B+CDT‒ (30.4%). All isolates were susceptible to metronidazole and vancomycin, and resistant to cefotaxime and gentamicin, and 76.2% were multidrug resistant (MDR). RT078/ST11/Clade 5 was the most common genotype (47.8%), which was also found in animals and humans worldwide. All RT078/ST11/Clade 5 strains were toxigenic and had deletions of the tcdC gene. About half of these strains were resistant to moxifloxacin, and 63.6% were MDR. CONCLUSIONS: C. difficile isolates in this study consisted mostly of toxigenic and MDR strains, and their genetic properties were highly similar to human C. difficile isolates. These results suggest high possibilities of zoonotic transmission and can provide knowledge for establishing strategies for the treatment and prevention of C. difficile infection.

A Rare Skeletal Disorder, Fibrous Dysplasia: A Review of Its Pathogenesis and Therapeutic Prospects.

Fibrous dysplasia (FD) is a rare, non-hereditary skeletal disorder characterized by its chronic course of non-neoplastic fibrous tissue buildup in place of healthy bone. A myriad of factors have been associated with its onset and progression. Perturbation of cell-cell signaling networks and response outputs leading to disrupted building blocks, incoherent multi-level organization, and loss of rigid structural motifs in mineralized tissues are factors that have been identified to participate in FD induction. In more recent years, novel insights into the unique biology of FD are transforming our understandings of its pathology, natural discourse of the disease, and treatment prospects. Herein, we built upon existing knowledge with recent findings to review clinical, etiologic, and histological features of FD and discussed known and potential mechanisms underlying FD manifestations. Subsequently, we ended on a note of optimism by highlighting emerging therapeutic approaches aimed at either halting or ameliorating disease progression.

Operational Definition Identifying Osteoporotic Vertebral Fractures in the Claims Database.

BACKGROUND: We analyzed the International Classification of Diseases, 10th edition (ICD-10) diagnostic codes, procedure codes, and radiographic image codes for vertebral fracture (VF) used in the database of Health Insurance Review and Assessment Service (HIRA) of Korea to establish a validated operational definition for identifying patients with osteoporotic VF in claims data. METHODS: We developed three operational definitions for detecting VFs using 9 diagnostic codes, 5 procedure codes and 4 imaging codes. Medical records and radiographs of 2,819 patients, who had primary and subordinated codes of VF between January 2016 and December 2016 at two institutions, were reviewed to detect true vertebral fractures. We evaluated the sensitivity and positive predictive value (PPV) of the operational definition in detecting true osteoporotic VF and obtained the receiver operating characteristic (ROC) curve. RESULTS: Among the 2,819 patients who had primary or secondary diagnosis codes for VF, 995 patients satisfied at least one of the criteria for the operational definition of osteoporotic VF. Of these patients, 594 were judged as having true fractures based on medical records and radiographic examinations. The sensitivity and PPV were 62.5 (95% confidence interval [CI], 59.4-65.6) and 59.7(95% CI, 56.6-62.8) respectively. In the receiver operating characteristic analysis, area under the curve (AUC) was 0.706 (95% CI, 0.688-0.724). CONCLUSION: Our findings demonstrate the validity of our operational definitions to identify VFs more accurately using claims data. This algorithm to identify VF is likely to be useful in future studies for diagnosing osteoporotic VF.

Accuracy of implant impression techniques with a scannable healing abutment.

STATEMENT OF PROBLEM: Scannable healing abutments are a convenient option to facilitate impression making for implant-supported restorations. However, studies evaluating the accuracy of the impression technique with scannable healing abutments are lacking. PURPOSE: The purpose of this in vitro study was to evaluate the accuracy of implant impression techniques with scannable healing abutments. MATERIALS AND METHODS: A partially edentulous mandibular dentiform model was fabricated with an epoxy resin, and implants were placed in the mandibular right second premolar and first molar areas. A maxillary dentiform model was then fabricated, and both models were mounted on an articulator. Scan data were obtained from the mounted models and set as the reference scans. The experimental models were divided into 4 groups (n=10). The conventional pick-up impression technique and definitive casts were used in group CI. The scan data from the definitive casts were obtained with a 3D model scanner. An intraoral scanner with a digital body scan was used in group DS. Group MS yielded definitive casts with dual-arch impressions with scannable healing abutments. The fabricated definitive casts were mounted and scanned with a 3D cast scanner. Intraoral scanning with scannable healing abutments was used in group IS. In all 4 groups, the interarch relationship in the maximum intercuspal position was obtained by scanning the facial aspect. The center of the implant head was set as a measurement point for linear intra-arch deviations and implant angle deviations. The mesiopalatal cusp tip of the maxillary right first molar was used to calibrate the linear interarch deviations. The data obtained from each group were compared with the data from the reference scan. As the data were not normally distributed, the Kruskal-Wallis test and Bonferroni correction were used for the analysis (α=.05). RESULTS: Group MS exhibited significantly higher deviations in linear intra-arch and implant angles compared with the other groups (P<.05). No significant difference was found between the groups in linear interarch deviations (P>.05). CONCLUSIONS: The accuracy of intraoral scanning with scannable healing abutments was comparable with that of conventional pick-up impression techniques and digital scans with scan bodies. However, model scanning with scannable healing abutments may not be clinically acceptable for implant impressions.

Clinical cases of zoonotic Cryptosporidium parvum (subtype IIdA15G1) infections in Korean goats.

Cryptosporidium parvum is an enteric protozoan, which causes severe diarrhoea in a wide range of vertebrate hosts including ruminants and humans. C. parvum infections are responsible for immense economic losses to the livestock industry; furthermore, the zoonotic spread of the infection may lead to mortality in immunosuppressed humans. In the present study, we report two cases of severe cryptosporidiosis in goat kids in the Republic of Korea. Both cases were afflicted with severe diarrhoea upon presentation; the histopathological examinations revealed atrophied and fused intestinal villi and numerous circular basophilic organisms in the jejunum and ileum. Both cases were diagnosed with cryptosporidiosis based on the results of the histopathological analysis, amplification of the C. parvum gp60 gene, modified Ziehl-Neelsen staining, and C. parvum antigen ELISA. According to the phylogenetic analysis using the C. parvum gp60 gene for the genetic subtypes, the C. parvum isolates were identified as subtype IIdA15G1 with zoonotic potential. This is the first pathological report of caprine cryptosporidiosis induced by C. parvum subtype IId in the Republic of Korea. Considering the clinical manifestations associated with the pathological lesions and the zoonotic significance of these findings, the continuous monitoring and prevention of C. parvum infections in goats are essential for minimising the economic losses in ruminant farms and in maintaining public health safety standards.